rs7940107

Variant names:

• chr11-69260303-G-A
• rs7940107

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.198 in 152,036 control chromosomes in the GnomAD database, including 3,590 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.20 (3590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.468

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.316 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30020 AN: 151918 Hom.: 3577 Cov.: 32

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.0118

Gnomad SAS AF: 0.0448

Gnomad FIN AF: 0.0665

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.212

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.198 AC: 30066 AN: 152036 Hom.: 3590 Cov.: 32 AF XY: 0.187 AC XY: 13893 AN XY: 74306

Gnomad4 AFR AF: 0.321

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.226

Gnomad4 EAS AF: 0.0120

Gnomad4 SAS AF: 0.0438

Gnomad4 FIN AF: 0.0665

Gnomad4 NFE AF: 0.177

Gnomad4 OTH AF: 0.212

Alfa AF: 0.183 Hom.: 3045

Bravo AF: 0.213

Asia WGS AF: 0.0660 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.79
DANN	Benign	0.54

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs7940107; hg19: chr11-69027770;